Hi Laurel

if a subject dir already exists recon-all will exit unless you specify
-force. Alternatively you can try using the -make all flag, which should
rerun only the steps that are needed (assuming the reboot didn't happen
e.g. in the middle of writing a file)

cheers
Bruce
On Tue, 28 Jan 2020, Laurel Quinlan
wrote:

>
>         External Email - Use Caution        
>
> Hi Doug,
>
> Thanks for looking over that file. It is the correct recon-all file for one
> of the problem brains. I discovered that there was a system reboot of some
> sort when the recon-all was processing for these problem brains, so that is
> likely what caused the process to stop. How can I restart the recon-all
> process for these brains? I have tried just rerunning the recon-all command
> but the process exits within a few moments each time. I am wondering if
> there is something I need to delete that was partially processed during the
> first attempt.
>
> Thanks,
>
> Laurel 
>
> ____________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
> N.,Ph.D. <DGREVE@mgh.harvard.edu>
> Sent: Friday, January 24, 2020 9:34 AM
> To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
> mri_relabel_hypointensities  
> It did not look like there was an explicit error in that log file, it just
> stops at mris_volmask. Is that the right recon-all? Also, please just send
> the text file so that we don't have to unzip it.
>
> On 1/22/2020 4:39 PM, Laurel Quinlan wrote:
>
>               External Email - Use Caution        
>
> Hi FS Support,
>
> I have two brains for which recon-all exited with errors after I
> edited the wm.mgz volume. It seems that the problem occurs during the
> mri_segstats and mri_relabel_hypointensities steps (if I'm reading the
> output of the command "tail scripts/recon-all.log" correctly). I
> attached one of the recon-all.log files as a zipped txt file. Please
> let me know if you have troubleshooting suggestions.
>
> Thank you for your help!  
>
> Laurel Quinlan
> Research Specialist
> Center for Healthy Minds
> University of Wisconsin-Madison
>
>
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>
>